ArticleNucleic acids research2017
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.Current research in structural biology · 2024Article
- Interpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model.Biophysical journal · 2023Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.Nucleic acids research · 2021Article
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 2021Article
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model.Biophysical journal · 2020Article
- Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 · 2020Article
- Article
- EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm.BMC genomics · 2019Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
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3 authors.
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Abstract
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome.
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